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Butkiewicz D, Krześniak M, Gdowicz-Kłosok A, Składowski K, Rutkowski T. DNA Double-Strand Break Response and Repair Gene Polymorphisms May Influence Therapy Results and Prognosis in Head and Neck Cancer Patients. Cancers (Basel) 2023; 15:4972. [PMID: 37894339 PMCID: PMC10605140 DOI: 10.3390/cancers15204972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/05/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Radiotherapy and cisplatin-based chemotherapy belong to the main treatment modalities for head and neck squamous cell carcinoma (HNSCC) and induce cancer cell death by generating DNA damage, including the most severe double-strand breaks (DSBs). Alterations in DSB response and repair genes may affect individual DNA repair capacity and treatment sensitivity, contributing to the therapy resistance and poor prognosis often observed in HNSCC. In this study, we investigated the association of a panel of single-nucleotide polymorphisms (SNPs) in 20 DSB signaling and repair genes with therapy results and prognosis in 505 HNSCC patients treated non-surgically with DNA damage-inducing therapies. In the multivariate analysis, there were a total of 14 variants associated with overall, locoregional recurrence-free or metastasis-free survival. Moreover, we identified 10 of these SNPs as independent predictors of therapy failure and unfavorable prognosis in the whole group or in two treatment subgroups. These were MRE11 rs2155209, XRCC5 rs828907, RAD51 rs1801321, rs12593359, LIG4 rs1805388, CHEK1 rs558351, TP53 rs1042522, ATM rs1801516, XRCC6 rs2267437 and NBN rs2735383. Only CHEK1 rs558351 remained statistically significant after correcting for multiple testing. These results suggest that specific germline variants related to DSB response and repair may be potential genetic modifiers of therapy effects and disease progression in HNSCC treated with radiotherapy and cisplatin-based chemoradiation.
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Affiliation(s)
- Dorota Butkiewicz
- Center for Translational Research and Molecular Biology of Cancer, Maria Skłodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland
| | - Małgorzata Krześniak
- Center for Translational Research and Molecular Biology of Cancer, Maria Skłodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland
| | - Agnieszka Gdowicz-Kłosok
- Center for Translational Research and Molecular Biology of Cancer, Maria Skłodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland
| | - Krzysztof Składowski
- I Radiation and Clinical Oncology Department, Maria Skłodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland
| | - Tomasz Rutkowski
- I Radiation and Clinical Oncology Department, Maria Skłodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland
- Radiotherapy Department, Maria Skłodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland
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2
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Hernandez-Martinez JM, Rosell R, Arrieta O. Somatic and germline ATM variants in non-small-cell lung cancer: Therapeutic implications. Crit Rev Oncol Hematol 2023:104058. [PMID: 37343657 DOI: 10.1016/j.critrevonc.2023.104058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 06/16/2023] [Indexed: 06/23/2023] Open
Abstract
ATM is an apical kinase of the DNA damage response involved in the repair of DNA double-strand breaks. Germline ATM variants (gATM) have been associated with an increased risk of developing lung adenocarcinoma (LUAD), and approximately 9% of LUAD tumors harbor somatic ATM mutations (sATM). Biallelic carriers of pathogenic gATM exhibit a plethora of immunological abnormalities, but few studies have evaluated the contribution of immune dysfunction to lung cancer susceptibility. Indeed, little is known about the clinicopathological characteristics of lung cancer patients with sATM or gATM alterations. The introduction of targeted therapies and immunotherapies, and the increasing number of clinical trials evaluating treatment combinations, warrants a careful reexamination of the benefits and harms that different therapeutic approaches have had in lung cancer patients with sATM or gATM. This review will discuss the role of ATM in the pathogenesis of lung cancer, highlighting potential therapeutic approaches to manage ATM-deficient lung cancers.
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Affiliation(s)
- Juan-Manuel Hernandez-Martinez
- Thoracic Oncology Unit and Experimental Oncology Laboratory, Instituto Nacional de Cancerología de México (INCan); CONACYT-Instituto Nacional de Cancerología, Mexico City, Mexico
| | - Rafael Rosell
- Institut d'Investigació en Ciències Germans Trias i Pujol, Badalona, Spain; (4)Institut Català d'Oncologia, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Oscar Arrieta
- Thoracic Oncology Unit and Experimental Oncology Laboratory, Instituto Nacional de Cancerología de México (INCan).
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3
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The Effects of Cryogenic Storage on Human Dental Pulp Stem Cells. Int J Mol Sci 2021; 22:ijms22094432. [PMID: 33922674 PMCID: PMC8122943 DOI: 10.3390/ijms22094432] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/19/2021] [Accepted: 04/21/2021] [Indexed: 12/11/2022] Open
Abstract
Dental pulp stem cells (DPSCs) are a type of easily accessible adult mesenchymal stem cell. Due to their ease of access, DPSCs show great promise in regenerative medicine. However, the tooth extractions from which DPSCs can be obtained are usually performed at a period of life when donors would have no therapeutic need of them. For this reason, it is imperative that successful stem cell storage techniques are employed so that these cells remain viable for future use. Any such techniques must result in high post-thaw stem cell recovery without compromising stemness, proliferation, or multipotency. Uncontrolled-rate freezing is not a technically or financially demanding technique compared to expensive and laborious controlled-rate freezing techniques. This study was aimed at observing the effect of uncontrolled-rate freezing on DPSCs stored for 6 and 12 months. Dimethyl sulfoxide at a concentration of 10% was used as a cryoprotective agent. Various features such as shape, proliferation capacity, phenotype, and multipotency were studied after DPSC thawing. The DPSCs did not compromise their stemness, viability, proliferation, or differentiating capabilities, even after one year of cryopreservation at −80 °C. After thawing, they retained their stemness markers and low-level expression of hematopoietic markers. We observed a size reduction in recovery DPSCs after one year of storage. This observation indicates that DPSCs can be successfully used in potential clinical applications, even after a year of uncontrolled cryopreservation.
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Hulshof EC, Lim L, de Hingh IHJT, Gelderblom H, Guchelaar HJ, Deenen MJ. Genetic Variants in DNA Repair Pathways as Potential Biomarkers in Predicting Treatment Outcome of Intraperitoneal Chemotherapy in Patients With Colorectal Peritoneal Metastasis: A Systematic Review. Front Pharmacol 2020; 11:577968. [PMID: 33117169 PMCID: PMC7575928 DOI: 10.3389/fphar.2020.577968] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/27/2020] [Indexed: 12/18/2022] Open
Abstract
Background The introduction of cytoreductive surgery (CRS) followed by hyperthermic intraperitoneal chemotherapy (HIPEC) with either oxaliplatin or mitomycin C for patients with colorectal peritoneal metastasis (CPM) has resulted in a major increase in overall survival. Nonetheless, despite critical patient selection, the majority of patients will develop recurrent disease within one year following CRS + HIPEC. Therefore, improvement of patient and treatment selection is needed and may be achieved by the incorporation of genetic biomarkers. This systematic review aims to provide an overview of genetic biomarkers in the DNA repair pathway that are potentially predictive for treatment outcome of patients with colorectal peritoneal metastases treated with CRS + HIPEC with oxaliplatin or mitomycin C. Methods A systematic review was conducted according to the PRISMA guidelines. Given the limited number of genetic association studies of intraperitoneal mitomycin C and oxaliplatin in patients with CPM, we expanded the review and extrapolated the data from biomarker studies conducted in colorectal cancer patients treated with systemic mitomycin C– and oxaliplatin-based chemotherapy. Results In total, 43 papers were included in this review. No study reported potential pharmacogenomic biomarkers in patients with colorectal cancer undergoing mitomycin C–based chemotherapy. For oxaliplatin-based chemotherapy, a total of 26 genetic biomarkers within 14 genes were identified that were significantly associated with treatment outcome. The most promising genetic biomarkers were ERCC1 rs11615, XPC rs1043953, XPD rs13181, XPG rs17655, MNAT rs3783819/rs973063/rs4151330, MMR status, ATM protein expression, HIC1 tandem repeat D17S5, and PIN1 rs2233678. Conclusion Several genetic biomarkers have proven predictive value for the treatment outcome of systemically administered oxaliplatin. By extrapolation, these genetic biomarkers may also be predictive for the efficacy of intraperitoneal oxaliplatin. This should be the subject of further investigation.
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Affiliation(s)
- Emma C Hulshof
- Department of Clinical Pharmacy, Catharina Hospital, Eindhoven, Netherlands.,Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, Netherlands
| | - Lifani Lim
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, Netherlands
| | - Ignace H J T de Hingh
- Department of Surgical Oncology, Catharina Hospital, Eindhoven, Netherlands.,GROW, School for Oncology and Development Biology, Maastricht University, Maastricht, Netherlands
| | - Hans Gelderblom
- Department of Medical Oncology, Leiden University Medical Center, Leiden, Netherlands
| | - Henk-Jan Guchelaar
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, Netherlands.,Leiden Network for Personalized Therapeutics, Leiden, Netherlands
| | - Maarten J Deenen
- Department of Clinical Pharmacy, Catharina Hospital, Eindhoven, Netherlands.,Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, Netherlands
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5
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Mou J, Hu T, Wang Z, Chen W, Wang Y, Zhang W. ATM gene polymorphisms are associated with poor prognosis of non-small cell lung cancer receiving radiation therapy. Aging (Albany NY) 2020; 12:7465-7479. [PMID: 32329754 PMCID: PMC7202543 DOI: 10.18632/aging.103094] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 03/30/2020] [Indexed: 04/07/2023]
Abstract
We investigated the prognostic significance of ataxia telangiectasia mutated (ATM) single nucleotide polymorphisms (SNPs) in 720 Han Chinese non-small cell lung cancer (NSCLC) patients who underwent radiation or chemoradiation therapy. Kaplan-Meier survival curves showed that overall survival (OS) and disease-free survival (DFS) rates were significantly associated with two ATM SNPs, rs664143 and rs189037. Patients with the rs664143 GA or AA genotype had poorer DFS (hazard ratio (HR) = 1.40, 95% confidence interval (CI) = 1.05-1.86, P = 0.021) and OS (HR = 1.28, 95%CI = 1.12-1.78, P = 0.040) than those with the rs664143 GG phenotype. Patients with the rs189037 AG/GG genotypes had poorer prognoses than those with the rs189037 AA genotype (AG/GG vs. AA: DFS, HR = 1.44, 95%CI = 1.06-1.95, P=0.019; OS, HR = 1.16, 95%CI = 1.16-1.17-2.21, P=0.004). These results were confirmed by subgroup analysis based on clinical factors such as smoking, histology, tumor stage, treatment, and radiation dose, all of which were significantly associated with DFS and OS rates in NSCLC patients. These findings show that ATM rs664143 and rs189037 variants determine prognosis in NSCLC patients that have undergone radiation or chemoradiation therapies.
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Affiliation(s)
- Junjun Mou
- Department of Radiotherapy, Yantai Yuhuangding Hospital, The Affiliated Hospital of Qingdao University, Yantai 264000, Shandong, China
| | - Tao Hu
- Department of Thoracic Surgery, Yantai Yuhuangding Hospital, The Affiliated Hospital of Qingdao University, Yantai 264000, Shandong, China
| | - Zhiwu Wang
- Department of Chemoradiotherapy, Tangshan People’s Hospital, Tangshan 063000, China
| | - Wei Chen
- Training Department, Yantai Yuhuangding Hospital, The Affiliated Hospital of Qingdao University, Yantai 264000, Shandong, China
| | - Yang Wang
- Department of Radiotherapy, Yantai Yuhuangding Hospital, The Affiliated Hospital of Qingdao University, Yantai 264000, Shandong, China
| | - Wei Zhang
- Department of Radiotherapy, Yantai Yuhuangding Hospital, The Affiliated Hospital of Qingdao University, Yantai 264000, Shandong, China
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6
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Djansugurova L, Altynova N, Cherednichenko O, Khussainova E, Dubrova YE. The effects of DNA repair polymorphisms on chromosome aberrations in the population of Kazakhstan. Int J Radiat Biol 2020; 96:614-621. [PMID: 31914346 DOI: 10.1080/09553002.2020.1711460] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Purpose: To analyze the effects of DNA repair polymorphism and other factors on the frequency chromosome aberrations in an irradiated cohort of subjects living around the Semipalatinsk nuclear test site and non-exposed group of subjects from ecologically favorable zones of Kazakhstan.Materials and methods: Blood samples were collected in the rural areas of the East Kazakhstan district around the Semipalatinsk nuclear test site and ecologically favorable zones of Almaty region of Kazakhstan. Chromosome aberrations in the fresh and cryopreserved peripheral blood lymphocyte cultures were analyzed by Giemsa staining. Single nucleotide polymorphisms at eight DNA repair genes (XRCC1 rs1799782, XRCC1 rs25487, XRCC3 rs861539, ATM rs1801516, XPD rs1799793, XPD rs13181, APEX1 rs1130409, and hOGG1 rs1052133) were determined by PCR-RFLP method.Results: The age of donors and smoking significantly affected the frequency of chromosome aberrations among the irradiated and control subjects. In the irradiated and control cohorts, the frequency of chromosome aberrations was significantly increased in the heterozygous ATM rs1801516 (1853 Asp/Asn) individuals; for the rest of the loci no significant associations between polymorphism and the frequency of chromosome aberrations were detected.Conclusions: The age of donors, smoking, and the ATM rs1801516 polymorphism significantly affect the frequency of chromosome aberrations among individuals inhabiting contaminated area around the Semipalatinsk nuclear weapon test site, as well as among those inhabiting ecologically favorable zones of Kazakhstan.
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Affiliation(s)
- Leyla Djansugurova
- Laboratory of Molecular Genetics and Laboratory of Genetic Monitoring, Institute of General Genetics and Cytology, Almaty, Kazakhstan
| | - Nazym Altynova
- Laboratory of Molecular Genetics and Laboratory of Genetic Monitoring, Institute of General Genetics and Cytology, Almaty, Kazakhstan
| | - Oksana Cherednichenko
- Laboratory of Molecular Genetics and Laboratory of Genetic Monitoring, Institute of General Genetics and Cytology, Almaty, Kazakhstan
| | - Elmira Khussainova
- Laboratory of Molecular Genetics and Laboratory of Genetic Monitoring, Institute of General Genetics and Cytology, Almaty, Kazakhstan
| | - Yuri E Dubrova
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
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7
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Al-Shaheri FN, Al-Shami KM, Gamal EH, Mahasneh AA, Ayoub NM. Association of DNA repair gene polymorphisms with colorectal cancer risk and treatment outcomes. Exp Mol Pathol 2019; 113:104364. [PMID: 31881200 DOI: 10.1016/j.yexmp.2019.104364] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/16/2019] [Accepted: 12/24/2019] [Indexed: 02/07/2023]
Abstract
Colorectal cancer (CRC) is the third most common carcinoma worldwide. Despite the progress in screening and treatment, CRC remains a leading cause of cancer-related mortality. Alterations to normal nucleic acid processing may drive neoplastic transformation of colorectal epithelium. DNA repair machinery performs an essential function in the protection of genome by reducing the number of genetic polymorphisms/variations that may drive carcinogenicity. Four essential DNA repair systems are known which include nucleotide excision repair (NER), base excision repair (BER), mismatch repair (MMR), and double-strand break repair (DSBR). Polymorphisms of DNA repair genes have been shown to influence the risk of cancer development as well as outcomes of treatment. Several studies demonstrated the association between genetic polymorphism of DNA repair genes and increased risk of CRC in different populations. In this review, we have summarized the impact of DNA repair gene polymorphisms on risk of CRC development and treatment outcomes. Advancements of the current understanding for the impact of DNA repair gene polymorphisms on the risk and treatment of CRC may support diagnostic and predictive roles in patients with CRC.
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Affiliation(s)
- Fawaz N Al-Shaheri
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), ImNeuenheimer Feld 580, 69120 Heidelberg, Germany; Medical Faculty Heidelberg, University of Heidelberg, ImNeuenheimer Feld 672, 69120 Heidelberg, Germany; Faculty of Applied Medical Sciences, Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid, Jordan.
| | - Kamal M Al-Shami
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, 720 South Donahue Drive, Auburn, Alabama 36849, United States of America; Department of Clinical Pharmacy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid 22110, Jordan.
| | - Eshrak H Gamal
- Department of Oncology, Collage of Medicine, Bonn University, Germany; Faculty of Applied Medical Sciences, Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid, Jordan.
| | - Amjad A Mahasneh
- Department of Applied Biological Sciences, Faculty of Science and Arts, Jordan University of Science and Technology, Irbid 22110, Jordan.
| | - Nehad M Ayoub
- Department of Clinical Pharmacy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid 22110, Jordan.
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8
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Yang L, Xu M, Cui CB, Wei PH, Wu SZ, Cen ZJ, Meng XX, Huang QG, Xie ZC. Diagnostic and prognostic values of the mRNA expression of excision repair cross-complementation enzymes in hepatitis B virus-related hepatocellular carcinoma. Cancer Manag Res 2018; 10:5313-5328. [PMID: 30464628 PMCID: PMC6225908 DOI: 10.2147/cmar.s179043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Background The current study aims at using the whole genome expression profile chips for systematically investigating the diagnostic and prognostic values of excision repair cross-complementation (ERCC) genes in hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC). Materials and methods Whole genome expression profile chips were obtained from the GSE14520. The receiver-operating characteristic (ROC) curve, survival analysis, and nomogram were used to investigate the diagnostic and prognostic values of ERCC genes. Investigation of the potential function of ERCC8 was carried out by gene set enrichment analysis (GSEA) and genome-wide coexpression analysis. Results ROC analysis suggests that six ERCC genes (ERCC1, ERCC2, ERCC3, ERCC4, ERCC5, and ERCC8) were dysregulated and may have potential to distinguish between HBV-related HCC tumor and paracancerous tissues (area under the curve of ROC ranged from 0.623 to 0.744). Survival analysis demonstrated that high ERCC8 expression was associated with a significantly decreased risk of recurrence (adjusted P=0.021; HR=0.643; 95% CI=0.442–0.937) and death (adjusted P=0.049; HR=0.631; 95% CI=0.399–0.998) in HBV-related HCC. Then, we also developed two nomograms for the HBV-related HCC individualized prognosis predictions. GSEA suggests that the high expression of ERCC8 may have involvement in the energy metabolism biological processes. As the genome-wide coexpression analysis and functional assessment of ERCC8 suggest, those coexpressed genes were significantly enriched in multiple biological processes of DNA damage and repair. Conclusion The present study indicates that six ERCC genes (ERCC1, ERCC2, ERCC3, ERCC4, ERCC5, and ERCC8) were dysregulated between HBV-related HCC tumor and paracancerous tissues and that the mRNA expression of ERCC8 may serve as a potential biomarker for the HBV-related HCC prognosis.
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Affiliation(s)
- Lu Yang
- Department of Epidemiology, Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China,
| | - Ming Xu
- Department of Human Anatomy and Histology and Embryology, Qilu Medical University, Zibo 255213, Shandong Province, People's Republic of China
| | - Chuan-Bao Cui
- Department of Epidemiology, Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China,
| | - Peng-Hai Wei
- Department of Epidemiology, Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China,
| | - Shu-Zhi Wu
- Department of Epidemiology, Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China,
| | - Zuo-Jie Cen
- Department of Epidemiology, Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China,
| | - Xing-Xing Meng
- Department of Epidemiology, Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China,
| | - Qiong-Guang Huang
- Department of Epidemiology, Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China,
| | - Zhi-Chun Xie
- Department of Epidemiology, Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China,
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9
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Rafnar T, Gunnarsson B, Stefansson OA, Sulem P, Ingason A, Frigge ML, Stefansdottir L, Sigurdsson JK, Tragante V, Steinthorsdottir V, Styrkarsdottir U, Stacey SN, Gudmundsson J, Arnadottir GA, Oddsson A, Zink F, Halldorsson G, Sveinbjornsson G, Kristjansson RP, Davidsson OB, Salvarsdottir A, Thoroddsen A, Helgadottir EA, Kristjansdottir K, Ingthorsson O, Gudmundsson V, Geirsson RT, Arnadottir R, Gudbjartsson DF, Masson G, Asselbergs FW, Jonasson JG, Olafsson K, Thorsteinsdottir U, Halldorsson BV, Thorleifsson G, Stefansson K. Variants associating with uterine leiomyoma highlight genetic background shared by various cancers and hormone-related traits. Nat Commun 2018; 9:3636. [PMID: 30194396 PMCID: PMC6128903 DOI: 10.1038/s41467-018-05428-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 07/02/2018] [Indexed: 01/12/2023] Open
Abstract
Uterine leiomyomas are common benign tumors of the myometrium. We performed a meta-analysis of two genome-wide association studies of leiomyoma in European women (16,595 cases and 523,330 controls), uncovering 21 variants at 16 loci that associate with the disease. Five variants were previously reported to confer risk of various malignant or benign tumors (rs78378222 in TP53, rs10069690 in TERT, rs1800057 and rs1801516 in ATM, and rs7907606 at OBFC1) and four signals are located at established risk loci for hormone-related traits (endometriosis and breast cancer) at 1q36.12 (CDC42/WNT4), 2p25.1 (GREB1), 20p12.3 (MCM8), and 6q26.2 (SYNE1/ESR1). Polygenic score for leiomyoma, computed using UKB data, is significantly correlated with risk of cancer in the Icelandic population. Functional annotation suggests that the non-coding risk variants affect multiple genes, including ESR1. Our results provide insights into the genetic background of leiomyoma that are shared by other benign and malignant tumors and highlight the role of hormones in leiomyoma growth. Uterine leiomyomas are common benign tumors. Here, a meta-analysis of two European leiomyoma GWAS uncovers 21 leiomyoma risk variants at 16 loci, providing evidence of genetic overlap between leiomyoma and various benign and malignant tumors and highlighting the role of estrogen in tumor growth.
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Affiliation(s)
- Thorunn Rafnar
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland.
| | | | | | - Patrick Sulem
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland
| | - Andres Ingason
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland
| | | | | | | | - Vinicius Tragante
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland.,Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, University of Utrecht, 3584 CX, Utrecht, The Netherlands
| | | | | | - Simon N Stacey
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland
| | | | | | | | - Florian Zink
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland
| | | | | | | | | | - Anna Salvarsdottir
- Department of Obstetrics and Gynecology, Landspitali University Hospital, 101, Reykjavik, Iceland
| | - Asgeir Thoroddsen
- Department of Obstetrics and Gynecology, Landspitali University Hospital, 101, Reykjavik, Iceland
| | - Elisabet A Helgadottir
- Department of Obstetrics and Gynecology, Landspitali University Hospital, 101, Reykjavik, Iceland
| | - Katrin Kristjansdottir
- Department of Obstetrics and Gynecology, Landspitali University Hospital, 101, Reykjavik, Iceland
| | - Orri Ingthorsson
- Department of Obstetrics and Gynecology, Akureyri Hospital, 600, Akureyri, Iceland
| | - Valur Gudmundsson
- Department of Obstetrics and Gynecology, Akureyri Hospital, 600, Akureyri, Iceland
| | - Reynir T Geirsson
- Department of Obstetrics and Gynecology, Landspitali University Hospital, 101, Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, 101, Reykjavik, Iceland
| | - Ragnheidur Arnadottir
- Department of Obstetrics and Gynecology, Landspitali University Hospital, 101, Reykjavik, Iceland
| | - Daniel F Gudbjartsson
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland.,School of Engineering and Natural Sciences, University of Iceland, 101, Reykjavik, Iceland
| | - Gisli Masson
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland
| | - Folkert W Asselbergs
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, University of Utrecht, 3584 CX, Utrecht, The Netherlands.,Durrer Center for Cardiovascular Research, Netherlands Heart Institute, 3501 DG, Utrecht, The Netherlands.,Institute of Cardiovascular Science, Faculty of Population Health Sciences, University College London, London, WC1E 6HX, UK.,Farr Institute of Health Informatics Research and Institute of Health Informatics, University College London, London, NW1 2DA, UK
| | - Jon G Jonasson
- Faculty of Medicine, School of Health Sciences, University of Iceland, 101, Reykjavik, Iceland.,Department of Pathology, Landspitali University Hospital, 101, Reykjavik, Iceland
| | - Karl Olafsson
- Department of Obstetrics and Gynecology, Landspitali University Hospital, 101, Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, 101, Reykjavik, Iceland
| | - Bjarni V Halldorsson
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland.,School of Science and Engineering, Reykjavik University, 101, Reykjavik, Iceland
| | | | - Kari Stefansson
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland. .,Faculty of Medicine, School of Health Sciences, University of Iceland, 101, Reykjavik, Iceland.
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10
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Mirza-Aghazadeh-Attari M, Darband SG, Kaviani M, Mihanfar A, Aghazadeh Attari J, Yousefi B, Majidinia M. DNA damage response and repair in colorectal cancer: Defects, regulation and therapeutic implications. DNA Repair (Amst) 2018; 69:34-52. [PMID: 30055507 DOI: 10.1016/j.dnarep.2018.07.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/15/2018] [Accepted: 07/15/2018] [Indexed: 12/11/2022]
Abstract
DNA damage response, a key factor involved in maintaining genome integrity and stability, consists of several kinase-dependent signaling pathways, which sense and transduce DNA damage signal. The severity of damage appears to determine DNA damage responses, which can include cell cycle arrest, damage repair and apoptosis. A number of recent studies have demonstrated that defection in signaling through this network is thought to be an underlying mechanism behind the development and progression of various types of human malignancies, including colorectal cancer. In this review, colorectal cancer and its molecular pathology as well as DNA damage response is briefly introduced. Finally, the involvement of key components of this network in the initiation/progression, prognosis, response to treatment and development of drug resistance is comprehensively discussed.
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Affiliation(s)
- Mohammad Mirza-Aghazadeh-Attari
- Aging Research Institute, Tabriz University of Medical Sciences, Tabriz, Iran; Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Saber Ghazizadeh Darband
- Danesh Pey Hadi Co., Health Technology Development Center, Urmia University of Medical Sciences, Urmia, Iran
| | - Mojtaba Kaviani
- School of Nutrition and Dietetics, Acadia University, Wolfville, Nova Scotia, Canada
| | - Ainaz Mihanfar
- Stem Cell and Regenerative Medicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Bahman Yousefi
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Maryam Majidinia
- Solid Tumor Research Center, Urmia University of Medical Sciences, Urmia, Iran.
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11
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Palugulla S, Devaraju P, Kayal S, Narayan SK, Mathaiyan J. Genetic polymorphisms in cyclin H gene are associated with oxaliplatin-induced acute peripheral neuropathy in South Indian digestive tract cancer patients. Cancer Chemother Pharmacol 2018; 82:421-428. [PMID: 29936608 DOI: 10.1007/s00280-018-3629-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/18/2018] [Indexed: 02/01/2023]
Abstract
PURPOSE Digestive tract cancer patients treated with oxaliplatin are often associated with the development of peripheral neuropathy. The aim of the present study is to identify the influence of single-nucleotide polymorphisms (SNPs) in genes involved in oxaliplatin metabolism, cell cycle control, detoxification or excretion pathways with the development of oxaliplatin-induced acute peripheral neuropathy (acute OXAIPN) and its severity among digestive tract cancer patients treated with oxaliplatin-based chemotherapy. PATIENTS AND METHODS A total of 228 digestive tract cancer patients undergoing with the oxaliplatin-based chemotherapy between November 2014 and December 2016 were included in the current study. Genomic DNA was extracted from peripheral blood by standard phenol-chloroform method. Genotyping of five SNPs in four genes [GSTP1 (rs1965), ABCG2 (rs3114018), CCNH (rs2230641, rs3093816), AGXT (rs4426527)] was carried out by Real-Time TaqMan SNP genotyping assay. RESULTS We found that the two genetic variants rs2230641 and rs3093816 in cyclin H (CCNH) gene were significantly associated with both the incidence and severity of acute OXAIPN. For CCNH-rs2230641 (AA vs AG+GG; dominant model) Incidence: OR 2.62, 95% CI 1.44-4.75, p = 0.001, severity; OR 4.64, 95% CI 1.58-13.62, p = 0.002. For CCNH-rs3093816 (AA vs AG+GG; dominant model); incidence: OR 3.43, 95% CI 1.57-7.50, p = 0.001; severity: OR 2.36, 95% CI 1.05-5.30, p = 0.033. CONCLUSIONS The results of the present study found significant association between CCNH polymorphisms and acute OXAIPN development. However, further studies are warranted from independent groups to validate our study results.
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Affiliation(s)
- Sreenivasulu Palugulla
- Department of Pharmacology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Pondicherry, 605006, India
| | - Panneer Devaraju
- Unit of Microbiology and Molecular Biology, Vector Control Research Centre, Indian Council of Medical Research, Pondicherry, 605006, India
| | - Smita Kayal
- Department of Medical Oncology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Pondicherry, 605006, India
| | - Sunil K Narayan
- Department of Neurology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Pondicherry, 605006, India
| | - Jayanthi Mathaiyan
- Department of Pharmacology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Pondicherry, 605006, India.
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12
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Xu M, Liu Y, Li D, Wang X, Liang S, Zhang G, Yang X. Chinese C allele carriers of the ERCC5 rs1047768 polymorphism are more sensitive to platinum-based chemotherapy: a meta-analysis. Oncotarget 2018; 9:1248-1256. [PMID: 29416691 PMCID: PMC5787435 DOI: 10.18632/oncotarget.18981] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 06/17/2017] [Indexed: 12/11/2022] Open
Abstract
It is suspected that ERCC5 rs1047768 and rs17655 polymorphisms influence the response to platinum-based chemotherapy. This meta-analysis was performed to summarize the scattered evidence regarding the association between these two polymorphisms and sensitivity to platinum-based treatment. Thirteen studies were included after a comprehensive literature search. The pooled odds ratios and 95% confidence intervals suggested that the C allele of the ERCC5 rs1047768 polymorphism is associated with elevated sensitivity to platinating agents, especially for Chinese patients. However, no difference among rs17655 genotypes could be detected.
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Affiliation(s)
- Meizhen Xu
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Yina Liu
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Dan Li
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China.,School of Life Science and Technology, Tongji University, Shanghai, China.,Present address: Jiayin BioTechnology Co., Ltd., Shanghai, China
| | | | | | - Gaochuan Zhang
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Xiaoqin Yang
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
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13
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Bahrami A, Amerizadeh F, Hassanian SM, ShahidSales S, Khazaei M, Maftouh M, Ghayour-Mobarhan M, Ferns GA, Avan A. Genetic variants as potential predictive biomarkers in advanced colorectal cancer patients treated with oxaliplatin-based chemotherapy. J Cell Physiol 2017; 233:2193-2201. [DOI: 10.1002/jcp.25966] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 04/18/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Afsane Bahrami
- Department of Modern Sciences and Technologies; Faculty of Medicine, Mashhad University of Medical Sciences; Mashhad Iran
- Student Research Committee, Faculty of Medicine; Mashhad University of Medical Sciences; Mashhad Iran
| | - Forouzan Amerizadeh
- Department of Modern Sciences and Technologies; Faculty of Medicine, Mashhad University of Medical Sciences; Mashhad Iran
- Student Research Committee, Faculty of Medicine; Mashhad University of Medical Sciences; Mashhad Iran
| | - Seyed Mahdi Hassanian
- Metabolic Syndrome Research Center; Mashhad University of Medical Sciences; Mashhad Iran
- Department of Medical Biochemistry, Faculty of Medicine; Mashhad University of Medical Sciences; Mashhad Iran
| | | | - Majid Khazaei
- Department of Physiology, Faculty of Medicine; Mashhad University of Medical Sciences; Mashhad Iran
| | - Mina Maftouh
- Metabolic Syndrome Research Center; Mashhad University of Medical Sciences; Mashhad Iran
| | - Majid Ghayour-Mobarhan
- Metabolic Syndrome Research Center; Mashhad University of Medical Sciences; Mashhad Iran
| | - Gordon A. Ferns
- Brighton & Sussex Medical School; Division of Medical Education; Falmer Brighton, Sussex UK
| | - Amir Avan
- Metabolic Syndrome Research Center; Mashhad University of Medical Sciences; Mashhad Iran
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14
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Zhou F, Zhu M, Wang M, Qiu L, Cheng L, Jia M, Xiang J, Wei Q. Genetic variants of DNA repair genes predict the survival of patients with esophageal squamous cell cancer receiving platinum-based adjuvant chemotherapy. J Transl Med 2016; 14:154. [PMID: 27246611 PMCID: PMC4888614 DOI: 10.1186/s12967-016-0903-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 05/12/2016] [Indexed: 12/20/2022] Open
Abstract
Background Adjuvant chemotherapy in patients with resected esophageal squamous cell cancer (ESCC) remains controversial for its uncertain role in improving overall survival (OS). Nucleotide excision repair (NER) removes DNA-adducts in tumor cells induced by the platinum-based chemotherapy and thus may modulate efficacy of the treatment. The present study evaluated if single nucleotide polymorphisms (SNPs) of NER genes were prognostic biomarkers in ESCC patients treated with platinum-based adjuvant chemotherapy (PAC). Methods The analysis included 572 patients, for whom six SNPs of NER genes [i.e., XPC (rs1870134 and rs2228001), ERCC2/XPD rs238406 and ERCC5/XPG (rs2094258, rs2296147 and rs873601)] were detected with the TaqMan assay. Kaplan–Meier analyses and Cox proportional hazards models were used to evaluate their associations with disease free survival (DFS) and OS of these ESCC patients receiving PAC. Receiving operating characteristic curve analysis was used to evaluate the role of the risk genotypes in the DFS and OS. Results We found that ERCC5/XPG rs2094258 and rs873601 and ERCC2/XPD rs238406 SNPs were independently associated with poorer DFS and OS of ESCC patients [ERCC5/XPG rs2094258: CT+TT vs. CC: adjusted hazards ratio (adjHR) = 1.68 and P = 0.012 for DFS; adjHR = 1.99 and P = 0.0001 for OS; ERCC5/XPG rs873601: GA+GG vs. AA: adjHR = 1.59 and P = 0.024 for DFS; adjHR = 1.91 and P = 0.0005 for OS; ERCC2/XPD rs238406: TT vs. GG+GT: adjHR = 1.43 and P = 0.020 for DFS; adjHR = 1.52 and P = 0.008 for OS]. These HRs increased as the number of risk genotypes increased in the combined analysis. The model combining the risk genotypes with clinical characteristics or the TNM stage system was better in predicting outcomes in ESCC patients with PAC. Conclusion SNPs of ERCC2/XPD and ERCC5/XPG may independently and jointly predict survival of ESCC patients treated with PAC in this study population. Further validation in other study populations is warranted. Electronic supplementary material The online version of this article (doi:10.1186/s12967-016-0903-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fei Zhou
- Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Fudan University Shanghai Medical College, Shanghai, China.,Department of Oncology, Shanghai Jiaotong University Affiliated Shanghai First People's Hospital, Shanghai, China
| | - Meiling Zhu
- Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Fudan University Shanghai Medical College, Shanghai, China.,Department of Oncology, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, China
| | - Mengyun Wang
- Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Fudan University Shanghai Medical College, Shanghai, China
| | - Lixin Qiu
- Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Fudan University Shanghai Medical College, Shanghai, China
| | - Lei Cheng
- Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Ming Jia
- Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Fudan University Shanghai Medical College, Shanghai, China
| | - Jiaqing Xiang
- Department of Oncology, Fudan University Shanghai Medical College, Shanghai, China. .,Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
| | - Qingyi Wei
- Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China. .,Duke Cancer Institute, Duke University Medical Center, 10 Bryn Searle Dr., Durham, NC, 27710, USA.
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15
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Kap EJ, Popanda O, Chang-Claude J. Nucleotide excision repair and response and survival to chemotherapy in colorectal cancer patients. Pharmacogenomics 2016; 17:755-94. [DOI: 10.2217/pgs-2015-0017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Several new chemotherapeutic agents have become available for the treatment of colorectal cancer, which has led to increased complexity in treatment planning. Treatment decision making for individual patients could be facilitated if guided by predictive and prognostic markers. As most cytotoxic drugs induce DNA damage, the DNA damage repair pathways hold potential for yielding such biomarkers. Here, we review the current evidence of a possible involvement of the nucleotide excision repair pathway in the efficacy of chemotherapeutic agents used in the treatment of colorectal cancer. Although a large number of studies have been conducted, they are generally of moderate size and heterogeneous in design. Up to date no firm conclusions can be drawn to translate these results into the clinic. We recommend further comprehensive investigations of the nucleotide excision repair pathway in large patient studies that include both discovery and validation cohorts.
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Affiliation(s)
- Elisabeth J Kap
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120 Heidelberg, Germany
| | - Odilia Popanda
- Division of Epigenomics & Cancer Risk Factors, DKFZ, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120 Heidelberg, Germany
- University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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16
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van Os N, Roeleveld N, Weemaes C, Jongmans M, Janssens G, Taylor A, Hoogerbrugge N, Willemsen M. Health risks for ataxia-telangiectasia mutated heterozygotes: a systematic review, meta-analysis and evidence-based guideline. Clin Genet 2016; 90:105-17. [DOI: 10.1111/cge.12710] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Revised: 11/13/2015] [Accepted: 12/07/2015] [Indexed: 01/03/2023]
Affiliation(s)
- N.J.H. van Os
- Department of Neurology - Pediatric Neurology, Donders Institute for Brain, Cognition and Behaviour; Nijmegen The Netherlands
| | - N. Roeleveld
- Department for Health Evidence, Radboud Institute for Health Sciences; Nijmegen The Netherlands
- Department of Pediatrics, Radboudumc Amalia Children's Hospital; Nijmegen The Netherlands
| | - C.M.R. Weemaes
- Department of Pediatrics, Radboudumc Amalia Children's Hospital; Nijmegen The Netherlands
| | - M.C.J. Jongmans
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences; Radboud university medical center; Nijmegen The Netherlands
| | - G.O. Janssens
- Department of Radiation Oncology; University Medical Center Utrecht and Princess Maxima Center for Pediatric Oncology; Utrecht The Netherlands
| | - A.M.R. Taylor
- School of Cancer Sciences; University of Birmingham; Birmingham UK
| | - N. Hoogerbrugge
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences; Radboud university medical center; Nijmegen The Netherlands
| | - M.A.A.P. Willemsen
- Department of Neurology - Pediatric Neurology, Donders Institute for Brain, Cognition and Behaviour; Nijmegen The Netherlands
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17
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Du Z, Zhang W, Zhou Y, Yu D, Chen X, Chang J, Qiao Y, Zhang M, Huang Y, Wu C, Xiao Z, Tan W, Lin D. Associations of ATM Polymorphisms With Survival in Advanced Esophageal Squamous Cell Carcinoma Patients Receiving Radiation Therapy. Int J Radiat Oncol Biol Phys 2015; 93:181-9. [PMID: 26094126 DOI: 10.1016/j.ijrobp.2015.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 04/02/2015] [Accepted: 05/01/2015] [Indexed: 10/23/2022]
Abstract
PURPOSE To investigate whether single nucleotide polymorphisms (SNPs) in the ataxia telangiectasia mutated (ATM) gene are associated with survival in patients with esophageal squamous cell carcinoma (ESCC) receiving radiation therapy or chemoradiation therapy or surgery only. METHODS AND MATERIALS Four tagSNPs of ATM were genotyped in 412 individuals with clinical stage III or IV ESCC receiving radiation therapy or chemoradiation therapy, and in 388 individuals with stage I, II, or III ESCC treated with surgery only. Overall survival time of ESCC among different genotypes was estimated by Kaplan-Meier plot, and the significance was examined by log-rank test. The hazard ratios (HRs) and 95% confidence intervals (CIs) for death from ESCC among different genotypes were computed by a Cox proportional regression model. RESULTS We found 2 SNPs, rs664143 and rs664677, associated with survival time of ESCC patients receiving radiation therapy. Individuals with the rs664143A allele had poorer median survival time compared with the rs664143G allele (14.0 vs 20.0 months), with the HR for death being 1.45 (95% CI 1.12-1.89). Individuals with the rs664677C allele also had worse median survival time than those with the rs664677T allele (14.0 vs 23.5 months), with the HR of 1.57 (95% CI 1.18-2.08). Stratified analysis showed that these associations were present in both stage III and IV cancer and different radiation therapy techniques. Significant associations were also found between the SNPs and locosregional progression or progression-free survival. No association between these SNPs and survival time was detected in ESCC patients treated with surgery only. CONCLUSION These results suggest that the ATM polymorphisms might serve as independent biomarkers for predicting prognosis in ESCC patients receiving radiation therapy.
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Affiliation(s)
- Zhongli Du
- State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Department of Etiology and Carcinogenesis (Beijing Key Laboratory for Carcinogenesis and Cancer Prevention), Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wencheng Zhang
- Department of Radiation Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuling Zhou
- State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Department of Etiology and Carcinogenesis (Beijing Key Laboratory for Carcinogenesis and Cancer Prevention), Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Dianke Yu
- State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Department of Etiology and Carcinogenesis (Beijing Key Laboratory for Carcinogenesis and Cancer Prevention), Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiabin Chen
- State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Department of Etiology and Carcinogenesis (Beijing Key Laboratory for Carcinogenesis and Cancer Prevention), Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiang Chang
- State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Department of Etiology and Carcinogenesis (Beijing Key Laboratory for Carcinogenesis and Cancer Prevention), Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yan Qiao
- State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Department of Etiology and Carcinogenesis (Beijing Key Laboratory for Carcinogenesis and Cancer Prevention), Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Meng Zhang
- State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Department of Etiology and Carcinogenesis (Beijing Key Laboratory for Carcinogenesis and Cancer Prevention), Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ying Huang
- State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Department of Etiology and Carcinogenesis (Beijing Key Laboratory for Carcinogenesis and Cancer Prevention), Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chen Wu
- State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Department of Etiology and Carcinogenesis (Beijing Key Laboratory for Carcinogenesis and Cancer Prevention), Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zefen Xiao
- Department of Radiation Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Wen Tan
- State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Department of Etiology and Carcinogenesis (Beijing Key Laboratory for Carcinogenesis and Cancer Prevention), Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Dongxin Lin
- State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Department of Etiology and Carcinogenesis (Beijing Key Laboratory for Carcinogenesis and Cancer Prevention), Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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18
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De Mattia E, Cecchin E, Toffoli G. Pharmacogenomics of intrinsic and acquired pharmacoresistance in colorectal cancer: Toward targeted personalized therapy. Drug Resist Updat 2015; 20:39-70. [DOI: 10.1016/j.drup.2015.05.003] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 05/11/2015] [Accepted: 05/14/2015] [Indexed: 02/07/2023]
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19
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Liu YZ, Wang W, Jiang LQ. Capecitabine-based combination chemotherapy for advanced colon cancer: Curative effect and influence on serum VEGF, TNFα and IL-2 levels. Shijie Huaren Xiaohua Zazhi 2014; 22:5567-5571. [DOI: 10.11569/wcjd.v22.i35.5567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the clinical effect of capecitabine-based combination chemotherapy in patients with advanced colon carcinoma and its effects on serum levels of vascular endothelial growth factor (VEGF), tumor necrosis factor-α (TNF-α) and interleukin-2 (IL-2).
METHODS: Ninety patients with advanced colon carcinoma who met the inclusion criteria were divided into two groups equally according to therapeutic scheme. The control group was treated with 5-fluorouraci and oxaliplatin, while the observation group was treated with capecitabine and oxaliplatin. The curative efficacy, serum levels of VEGF, TNF-α, and IL-2, and the rates of adverse reactions were observed and compared.
RESULTS: The observation group had a therapeutic efficiency ratio (TER) of 75.6%, which was significantly higher than 53.3% in the control groups (P < 0.05). After treatment, concentration of serum VEGF, TNF-α and IL-2 in the two groups were all reduced (P < 0.05 for all). In comparison with the control group, concentration of VEGF was statistically lower, while concentrations of TNF-α and IL-2 were statistically higher in the observation group (P < 0.05 for all). As to adverse reactions, the rates of leucopenia, diarrhea, nausea, peripheral neuritis and alopecia were comparable between the two groups (P > 0.05 for all).
CONCLUSION: Combined treatment with capecitabine with oxaliplatin for advanced colon carcinoma is effective, which can increase TER, reduce tumor neovascularization and improve immunological function with minor adverse reactions.
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20
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Rao KS, Paul A, Kumar ASA, Umamaheswaran G, Dubashi B, Gunaseelan K, Dkhar SA. Allele and genotype distributions of DNA repair gene polymorphisms in South Indian healthy population. BIOMARKERS IN CANCER 2014; 6:29-35. [PMID: 25520562 PMCID: PMC4259864 DOI: 10.4137/bic.s19681] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 11/11/2014] [Accepted: 11/13/2014] [Indexed: 12/11/2022]
Abstract
Various DNA repair pathways protect the structural and chemical integrity of the human genome from environmental and endogenous threats. Polymorphisms of genes encoding the proteins involved in DNA repair have been found to be associated with cancer risk and chemotherapeutic response. In this study, we aim to establish the normative frequencies of DNA repair genes in South Indian healthy population and compare with HapMap populations. Genotyping was done on 128 healthy volunteers from South India, and the allele and genotype distributions were established. The minor allele frequency of Xeroderma pigmentosum group A (XPA) G23A, Excision repair cross-complementing 2 (ERCC2)/Xeroderma pigmentosum group D (XPD) Lys751Gln, Xeroderma pigmentosum group G (XPG) His46His, XPG Asp1104His, and X-ray repair cross-complementing group 1 (XRCC1) Arg399Gln polymorphisms were 49.2%, 36.3%, 48.0%, 23.0%, and 34.0% respectively. Ethnic variations were observed in the frequency distribution of these polymorphisms between the South Indians and other HapMap populations. The present work forms the groundwork for cancer association studies and biomarker identification for treatment response and prognosis.
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Affiliation(s)
- Katiboina Srinivasa Rao
- Department of Pharmacology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Pondicherry, India
| | - Abialbon Paul
- Department of Pharmacology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Pondicherry, India
| | - Annan Sudarsan Arun Kumar
- Department of Pharmacology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Pondicherry, India
| | - Gurusamy Umamaheswaran
- Department of Pharmacology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Pondicherry, India
| | - Biswajit Dubashi
- Department of Medical Oncology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Pondicherry, India
| | - Karunanithi Gunaseelan
- Department of Radiotherapy, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Pondicherry, India
| | - Steven Aibor Dkhar
- Department of Pharmacology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Pondicherry, India
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21
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Khrunin AV, Khokhrin DV, Moisseev AA, Gorbunova VA, Limborska SA. Pharmacogenomic assessment of cisplatin-based chemotherapy outcomes in ovarian cancer. Pharmacogenomics 2014; 15:329-37. [PMID: 24533712 DOI: 10.2217/pgs.13.237] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
AIM Cisplatin and its analogs are potent antitumor agents. However, their use is restricted by significant variability in tumor response and toxicity. There is a great need to identify genetic markers to predict the most important adverse events and patient outcomes. MATERIALS & METHODS We have evaluated the association between polymorphisms in 106 genes involved mainly in xenobiotic metabolism, DNA repair, the cell cycle and apoptosis, and outcomes in 104 ovarian cancer patients receiving cisplatin-cyclophosphamide chemotherapy. Arrayed primer extension technology was used to genotype 228 SNPs. RESULTS Ten SNPs in nine genes were found to be associated with one or more of the assessed clinical end points. SNPs in TPMT and NQO1 were significantly associated with progression-free survival. Polymorphisms in ERCC5, RAD52, MUTYH and LIG3 correlated with the occurrence of severe neutropenia. SNPs in NAT2 and EPHX1 were associated with anemia and nephrotoxicity, respectively. A SNP in ADH1C was correlated with complete tumor response. CONCLUSION The results obtained suggest that SNPs in different genes involved in drug metabolism can be important in identifying patients at risk for nonresponse to or toxicity from cisplatin-based treatment.
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Affiliation(s)
- Andrey V Khrunin
- Department of Molecular Bases of Human Genetics, Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov sq., 2, Moscow, Russia
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Panczyk M. Pharmacogenetics research on chemotherapy resistance in colorectal cancer over the last 20 years. World J Gastroenterol 2014; 20:9775-827. [PMID: 25110414 PMCID: PMC4123365 DOI: 10.3748/wjg.v20.i29.9775] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Revised: 01/17/2014] [Accepted: 04/21/2014] [Indexed: 02/07/2023] Open
Abstract
During the past two decades the first sequencing of the human genome was performed showing its high degree of inter-individual differentiation, as a result of large international research projects (Human Genome Project, the 1000 Genomes Project International HapMap Project, and Programs for Genomic Applications NHLBI-PGA). This period was also a time of intensive development of molecular biology techniques and enormous knowledge growth in the biology of cancer. For clinical use in the treatment of patients with colorectal cancer (CRC), in addition to fluoropyrimidines, another two new cytostatic drugs were allowed: irinotecan and oxaliplatin. Intensive research into new treatment regimens and a new generation of drugs used in targeted therapy has also been conducted. The last 20 years was a time of numerous in vitro and in vivo studies on the molecular basis of drug resistance. One of the most important factors limiting the effectiveness of chemotherapy is the primary and secondary resistance of cancer cells. Understanding the genetic factors and mechanisms that contribute to the lack of or low sensitivity of tumour tissue to cytostatics is a key element in the currently developing trend of personalized medicine. Scientists hope to increase the percentage of positive treatment response in CRC patients due to practical applications of pharmacogenetics/pharmacogenomics. Over the past 20 years the clinical usability of different predictive markers has been tested among which only a few have been confirmed to have high application potential. This review is a synthetic presentation of drug resistance in the context of CRC patient chemotherapy. The multifactorial nature and volume of the issues involved do not allow the author to present a comprehensive study on this subject in one review.
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Custodio A, Moreno-Rubio J, Aparicio J, Gallego-Plazas J, Yaya R, Maurel J, Higuera O, Burgos E, Ramos D, Calatrava A, Andrada E, López R, Moreno V, Madero R, Cejas P, Feliu J. Pharmacogenetic predictors of severe peripheral neuropathy in colon cancer patients treated with oxaliplatin-based adjuvant chemotherapy: a GEMCAD group study. Ann Oncol 2014; 25:398-403. [DOI: 10.1093/annonc/mdt546] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Sasaki Y, Osada S, Mori R, Imai H, Tanaka Y, Matsuhashi N, Okumura N, Nonaka K, Takahashi T, Yoshida K. Determining timing of hepatectomy for colorectal cancer with distant metastasis according to imaging-based tumor shrinkage ratio. Int J Med Sci 2013; 10:1231-41. [PMID: 23935401 PMCID: PMC3739023 DOI: 10.7150/ijms.6244] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 07/22/2013] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND The optimal timing of surgical resection of liver metastasis remains controversial, and guidelines regarding the upper limits of operative indications have not yet been defined. Surgical indication for metastasis from colorectal cancer (CLM) based on results of preoperative chemotherapy and RNF8 was investigated. METHODS Differences in CLM size on CT were evaluated as shrinkage rate/day by dividing tumor shrinkage rates by the interval in days between CT. Levels of RNF8 of resected colorectal cancer and CLM frozen specimen were detected. RESULTS When the cut line for shrinkage rate at 12 weeks was set at 0.35%, disease-free survival was significantly better in patients with a shrinkage rate >0.35% vs. ≤0.35% (p=0.003). RNF8 expression was significantly higher in Tis (p=0.001). In liver metastasis, RNF8 expression level was significantly lower in patients with partial response to FOLFOX than with stable disease, (p=0.017). CONCLUSIONS A strategy of FOLFOX administration for 12 weeks to patients with low RNF8 expression and hepatectomy planned after 4 weeks rest may be accepted as the best therapeutic option for treating CLM.
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Affiliation(s)
| | - Shinji Osada
- Surgical Oncology, Gifu University, Graduate School of Medicine
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Negandhi AA, Hyde A, Dicks E, Pollett W, Younghusband BH, Parfrey P, Green RC, Savas S. MTHFR Glu429Ala and ERCC5 His46His polymorphisms are associated with prognosis in colorectal cancer patients: analysis of two independent cohorts from Newfoundland. PLoS One 2013; 8:e61469. [PMID: 23626689 PMCID: PMC3634085 DOI: 10.1371/journal.pone.0061469] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 03/08/2013] [Indexed: 01/28/2023] Open
Abstract
Introduction In this study, 27 genetic polymorphisms that were previously reported to be associated with clinical outcomes in colorectal cancer patients were investigated in relation to overall survival (OS) and disease free survival (DFS) in colorectal cancer patients from Newfoundland. Methods The discovery and validation cohorts comprised of 532 and 252 patients, respectively. Genotypes of 27 polymorphisms were first obtained in the discovery cohort and survival analyses were performed assuming the co-dominant genetic model. Polymorphisms associated with disease outcomes in the discovery cohort were then investigated in the validation cohort. Results When adjusted for sex, age, tumor stage and microsatellite instability (MSI) status, four polymorphisms were independent predictors of OS in the discovery cohort MTHFR Glu429Ala (HR: 1.72, 95%CI: 1.04–2.84, p = 0.036), ERCC5 His46His (HR: 1.78, 95%CI: 1.15–2.76, p = 0.01), SERPINE1 −675indelG (HR: 0.52, 95%CI: 0.32–0.84, p = 0.008), and the homozygous deletion of GSTM1 gene (HR: 1.4, 95%CI: 1.03–1.92, p = 0.033). In the validation cohort, the MTHFR Glu429Ala polymorphism was associated with shorter OS (HR: 1.71, 95%CI: 1.18–2.49, p = 0.005), although with a different genotype than the discovery cohort (CC genotype in the discovery cohort and AC genotype in the validation cohort). When stratified based on treatment with 5-Fluorouracil (5-FU)-based regimens, this polymorphism was associated with reduced OS only in patients not treated with 5-FU. In the DFS analysis, when adjusted for other variables, the TT genotype of the ERCC5 His46His polymorphism was associated with shorter DFS in both cohorts (discovery cohort: HR: 1.54, 95%CI: 1.04–2.29, p = 0.032 and replication cohort: HR: 1.81, 95%CI: 1.11–2.94, p = 0.018). Conclusions In this study, associations of the MTHFR Glu429Ala polymorphism with OS and the ERCC5 His46His polymorphism with DFS were identified in two colorectal cancer patient cohorts. Our results also suggest that the MTHFR Glu429Ala polymorphism may be an adverse prognostic marker in patients not treated with 5-FU.
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Affiliation(s)
- Amit A. Negandhi
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Angela Hyde
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Elizabeth Dicks
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - William Pollett
- Discipline of Surgery, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Banfield H. Younghusband
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Patrick Parfrey
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Roger C. Green
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Sevtap Savas
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
- Discipline of Oncology, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
- * E-mail:
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Wang J, Wang C, Gao Y, Lan XY, Lei CZ, Wang JQ, Chen H. Impacts of single nucleotide polymorphisms and haplotypes in the bovine Dapper1 gene on body weight. GENETICS AND MOLECULAR RESEARCH 2013; 12:1254-68. [DOI: 10.4238/2013.april.17.4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Zhang L, Gao G, Li X, Ren S, Li A, Xu J, Zhang J, Zhou C. Association between single nucleotide polymorphisms (SNPs) and toxicity of advanced non-small-cell lung cancer patients treated with chemotherapy. PLoS One 2012; 7:e48350. [PMID: 23118991 PMCID: PMC3485208 DOI: 10.1371/journal.pone.0048350] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 09/24/2012] [Indexed: 12/31/2022] Open
Abstract
New therapeutic approaches are being developed based on the findings that several genetic abnormalities underlying non-small-cell lung cancer (NSCLC) could influence chemosensitivity. In this study, we assessed whether polymorphisms in genes of nucleotide excision repair (NER) pathway, including ERCC5, ERCC6, MMS19L, CCNH, XPC, RRM1, can affect the tolerability of platinum-based chemotherapy in NSCLC patients. We used AllGloTM probe to assess genotyping and polymorphisms in 388 stage IIIB and IV NSCLC patients treated with platinum-based chemotherapy. MMS19L might be associated with the adverse events of chemotherapy in NSCLC, especially for all grade leucopenia (P = 0.020), all grade jaundice (P = 0.037) and all grade creatinine increasing (P = 0.013). In terms of grade 3/4 adverse events, MMS19L was related with total grade 3/4 adverse events (P = 0.024) and grade 3/4 thrombocytopenia (P = 0.035), while RRM1 was related with total grade 3/4 adverse events (P = 0.047) and grade 3/4 vomiting (P = 0.046). ERCC5 was related with more infection (P = 0.017). We found that some SNPs in NER pathway genes were correlated with toxicity treated with double chemotherapy in advanced NSCLC patients, especially for SNPs of MMS19L, RRM1 and ERCC5.
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Affiliation(s)
- Ling Zhang
- Department of Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Tongji University Cancer Institute, Shanghai, China
| | - Guanghui Gao
- Department of Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Tongji University Cancer Institute, Shanghai, China
| | - Xuefei Li
- Department of Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Tongji University Cancer Institute, Shanghai, China
| | - Shengxiang Ren
- Department of Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Tongji University Cancer Institute, Shanghai, China
| | - Aiwu Li
- Department of Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Tongji University Cancer Institute, Shanghai, China
| | - Jianfang Xu
- Department of Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Tongji University Cancer Institute, Shanghai, China
| | - Jie Zhang
- Department of Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Tongji University Cancer Institute, Shanghai, China
| | - Caicun Zhou
- Department of Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Tongji University Cancer Institute, Shanghai, China
- * E-mail:
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Wen Z, Liu ZP, Liu Z, Zhang Y, Chen L. An integrated approach to identify causal network modules of complex diseases with application to colorectal cancer. J Am Med Inform Assoc 2012; 20:659-67. [PMID: 22967703 DOI: 10.1136/amiajnl-2012-001168] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Many methods have been developed to identify disease genes and further module biomarkers of complex diseases based on gene expression data. It is generally difficult to distinguish whether the variations in gene expression are causative or merely the effect of a disease. The limitation of relying on gene expression data alone highlights the need to develop new approaches that can explore various data to reflect the casual relationship between network modules and disease traits. METHODS In this work, we developed a novel network-based approach to identify putative causal module biomarkers of complex diseases by integrating heterogeneous information, for example, epigenomic data, gene expression data, and protein-protein interaction network. We first formulated the identification of modules as a mathematical programming problem, which can be solved efficiently and effectively in an accurate manner. Then, we applied our approach to colorectal cancer (CRC) and identified several network modules that can serve as potential module biomarkers for characterizing CRC. Further validations using three additional gene expression datasets verified their candidate biomarker properties and the effectiveness of the method. Functional enrichment analysis also revealed that the identified modules are strongly related to hallmarks of cancer, and the enriched functions, such as inflammatory response, receptor and signaling pathways, are specific to CRC. RESULTS Through constructing a transcription factor (TF)-module network, we found that aberrant DNA methylation of genes encoding TF considerably contributes to the activity change of some genes, which may function as causal genes of CRC, and that can also be exploited to develop efficient therapies or effective drugs. CONCLUSION Our method can potentially be extended to the study of other complex diseases and the multiclassification problem.
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Affiliation(s)
- Zhenshu Wen
- Key Laboratory of Systems Biology, SIBS-Novo Nordisk Translational Research Centre for PreDiabetes, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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Can population differences in chemotherapy outcomes be inferred from differences in pharmacogenetic frequencies? THE PHARMACOGENOMICS JOURNAL 2012; 13:423-9. [PMID: 22733238 DOI: 10.1038/tpj.2012.26] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 05/04/2012] [Accepted: 05/07/2012] [Indexed: 02/06/2023]
Abstract
Inter-ethnic differences in drug handling and frequencies of pharmacogenetic variants are increasingly being characterized. In this study, we systematically assessed the feasibility of inferring ethnic trends in chemotherapy outcomes from inter-ethnic differences in pharmacogenetic variant frequencies. Frequencies of 51 variants and chemotherapy outcomes of East Asian and Caucasian colorectal cancer patients on standard chemotherapy regimens were summarized by meta-analyses, and variant frequencies were validated by MassARRAY analysis. Inferences of relative chemotherapy outcomes were made by considering minor allele function and population differences in their frequency. Significant population differences in genotype distributions were observed for 13/23 (60%) and 27/35 (77%) variants in the meta-analyses and validation series, respectively. Across chemotherapy regimens, East Asians had lower rates of grade 3/4 toxicity for diarrhea and stomatitis/mucositis than Caucasians, which was correctly inferred from 13/18 (72%, P=0.018) informative genetic variants. With appropriate variant selection, inferring relative population toxicity rates from population genotype differences may be relevant.
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Gao Y, Hayes RB, Huang WY, Caporaso NE, Burdette L, Yeager M, Chanock SJ, Berndt SI. DNA repair gene polymorphisms and tobacco smoking in the risk for colorectal adenomas. Carcinogenesis 2011; 32:882-7. [PMID: 21504893 DOI: 10.1093/carcin/bgr071] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
DNA damage is thought to play a critical role in the development of colorectal adenoma. Variation in DNA repair genes may alter their capacity to correct endogenous and exogenous DNA damage. We explored the association between common single-nucleotide polymorphisms (SNPs) in DNA repair genes and adenoma risk with a case-control study nested in the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial. A total of 1338 left sided, advanced colorectal adenoma cases and 1503 matched controls free of left-sided polyps were included in the study. Using DNA extracted from blood, 3144 tag SNPs in 149 DNA repair genes were successfully genotyped. Among Caucasians, 30 SNPs were associated with adenoma risk at P < 0.01, with four SNPs remaining significant after gene-based adjustment for multiple testing. The most significant finding was for a non-synonymous SNP (rs9350) in Exonuclease-1 (EXO1) [odds ratio (OR) = 1.30, 95% confidence interval (CI) = 1.11-1.51, P = 0.001)], which was predicted to be damaging using bioinformatics methods. However, the association was limited to smokers with a strong risk for current smokers (OR = 2.15, 95% CI = 1.27-3.65) and an intermediate risk for former smokers (OR = 1.45, 95% CI = 1.14-1.82) and no association for never smokers (OR = 0.98, 95% CI = 0.76-1.25) (P(interaction) = 0.002). Among the top findings, an SNP (rs17503908) in ataxia telangiectasia mutated (ATM) was inversely related to adenoma risk (OR = 0.75, 95% CI = 0.63-0.91). The association was restricted to never smokers (OR = 0.55, 95% CI = 0.40-0.76) with no increased risk observed among smokers (OR = 0.89, 95% CI = 0.70-1.13) (P(interaction) = 0.006). This large comprehensive study, which evaluated all presently known DNA repair genes, suggests that polymorphisms in EXO1 and ATM may be associated with risk for advanced colorectal adenoma with the associations modified by tobacco-smoking status.
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Affiliation(s)
- Ying Gao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-7236, USA.
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Regarding: 'Explorative study to identify novel candidate genes related to oxaliplatin efficacy and toxicity using a DNA repair array'. Br J Cancer 2010; 102:1791-2. [PMID: 20531418 PMCID: PMC2883708 DOI: 10.1038/sj.bjc.6605709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
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